I am pretty sure the great council decided that they could not have a queen, the Targaryens inheritance rule is unique to the rest of Westeros where daughters still come before brothers I believe.
In Game of Thrones Renly literally says "I'm 4th in line" - behind Joffrey, Tommen and Stannis. This is skipping Myrcella in favour of the brothers.
Because Dany is the last member of the Aerys line and she is a woman, they have to go back through all the male lines first to find a male, and they wouldn't find any still living, so they then have to go through the female lines in the hope of finding a male, which they would with the Baratheons. I thought they've made it quite clear in the Targaryens inheritance rules having a queen is an absolute last resort if there are literally no males.
I looked back into it, you're right that Renly would be fourth in line as the Iron Throne uses the Targaryen succession rules not the typical Andal succession rules that the rest of the realm uses, which would prefer a daughter of the direct line over a brother. For example, Edmure dies before he has a kid, and Catelyn would inherit Riverrun as the eldest remaining child of Hoster, not Brynden. For the Iron Throne though, a brother of the male line would have preference over a daughter, so Renly is ahead of Myrcella.
What you are saying about the Baratheons makes absolutely no sense with the type of succession you are claiming they practice. Either females have inheritance rights in some way, or they don't. You are trying to have it both ways here where Daenerys who is in direct line is excluded in favor of males descended from a female. If the inheritance rules prefers any male before a female, that would be any male through the male line, not a female line. The Baratheons are through a female line, which means they wouldn't have any legal claim on the throne through succession laws except in the absolute last resort (Robert's Targaryen heritage was used as a convenient reason after they had already won the Throne). It makes sense that you would go through all the male lines first to find a male successor, and when that fails you would then go through females, but the first person in the line of female succession is Daenerys, not Rhaelle. You can either inherit through females or you can't, but it would be a female within the male line. The Baratheons are not within the male line of Targaryen succession, which means despite being males they don't count in the line of succession unless every decedent in the male line is dead, which isn't the case.
EDIT: Here is the quote you are referencing, which means neither Daenerys nor the Baratheons have a legal claim on the Throne and that the line is officially dead without Jon Snow or (f)Aegon being legitimate.
In the eyes of many, the Great Council of 101 AC thereby established an iron precedent on matters of succession: regardless of seniority, the Iron Throne of Westeros could not pass to a woman, nor through a woman to her male descendents.
Regardless, it's essentially up for grabs by right of conquest as most titles have always been.